Author: bugman
Date: Mon Nov 26 17:59:56 2007
New Revision: 4055
URL: http://svn.gna.org/viewcvs/relax?rev=4055&view=rev
Log:
Added a set of unit tests for the data.align_tensor module and its class
methods.
Added:
branches/N_state_model/test_suite/unit_tests/_data/test_align_tensor.py
- copied, changed from r4053,
branches/N_state_model/test_suite/unit_tests/_data/test_diff_tensor.py
Copied:
branches/N_state_model/test_suite/unit_tests/_data/test_align_tensor.py (from
r4053, branches/N_state_model/test_suite/unit_tests/_data/test_diff_tensor.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_data/test_align_tensor.py?p2=branches/N_state_model/test_suite/unit_tests/_data/test_align_tensor.py&p1=branches/N_state_model/test_suite/unit_tests/_data/test_diff_tensor.py&r1=4053&r2=4055&rev=4055&view=diff
==============================================================================
--- branches/N_state_model/test_suite/unit_tests/_data/test_diff_tensor.py
(original)
+++ branches/N_state_model/test_suite/unit_tests/_data/test_align_tensor.py
Mon Nov 26 17:59:56 2007
@@ -26,291 +26,248 @@
from unittest import TestCase
# relax module imports.
-from data.diff_tensor import DiffTensorData, DiffTensorSimList
+from data.align_tensor import AlignTensorData, AlignTensorSimList
from relax_errors import RelaxError
-class Test_diff_tensor(TestCase):
- """Unit tests for the data.diff_tensor relax module."""
-
- def calc_spheroid_objects(self, tm, Da, theta, phi):
- """Function for calculating the spheroidal diffusion tensor
objects."""
+class Test_align_tensor(TestCase):
+ """Unit tests for the data.align_tensor relax module."""
+
+ def calc_objects(self, Axx, Ayy, Axy, Axz, Ayz):
+ """Function for calculating the alignment tensor objects."""
# The parameter values.
- Diso = 1/(6*tm)
- Dpar = Diso + 2.0/3.0 * Da
- Dper = Diso - 1.0/3.0 * Da
- Dratio = Dpar / Dper
-
- # Vectors.
- Dpar_unit = array([sin(theta) * cos(phi), sin(theta) * sin(phi),
cos(theta)])
+ Azz = 1.0 - Axx - Ayy
+ Axxyy = Axx - Ayy
# Matrices.
- tensor_diag = array([[ Dper, 0.0, 0.0],
- [ 0.0, Dper, 0.0],
- [ 0.0, 0.0, Dpar]])
- rotation = array([[ cos(theta) * cos(phi), -sin(phi), sin(theta) *
cos(phi) ],
- [ cos(theta) * sin(phi), cos(phi), sin(theta) *
sin(phi) ],
- [ -sin(theta), 0.0,
cos(theta) ]])
- tensor = dot(rotation, dot(tensor_diag, transpose(rotation)))
+ tensor_diag = array([[ Axx, 0.0, 0.0],
+ [ 0.0, Ayy, 0.0],
+ [ 0.0, 0.0, Azz]])
# Return the objects.
- return Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation,
tensor
+ return Azz, Axxyy, tensor_diag
def setUp(self):
- """Set 'self.diff_data' to an empty instance of the DiffTensorData
class."""
-
- self.diff_data = DiffTensorData()
-
-
- def test_append_spheroid_sim(self):
- """Test the appending of Monte Carlo simulation spheroidal diffusion
tensor parameters.
+ """Set 'self.align_data' to an empty instance of the AlignTensorData
class."""
+
+ self.align_data = AlignTensorData()
+
+
+ def test_append_sim(self):
+ """Test the appending of Monte Carlo simulation alignment tensor
parameters.
The following parameters will be appended to empty lists:
- tm: 8 ns
- Da: -1e7
- theta: 150 degrees
- phi: 30 degrees
+ Axx: -16.6278 Hz
+ Ayy: 6.13037 Hz
+ Axy: 7.65639 Hz
+ Axz: -1.89157 Hz
+ Ayz: 19.2561 Hz
"""
# The MC sim parameter values.
- tm = 8e-9
- Da = -1e7
- theta = (150 / 360.0) * 2.0 * pi
- phi = (30 / 360.0) * 2.0 * pi
-
- # Set the diffusion type.
- self.diff_data.type = 'spheroid'
-
- # Set the MC sim diffusion parameter lists.
- self.diff_data.tm_sim = DiffTensorSimList('tm', self.diff_data)
- self.diff_data.Da_sim = DiffTensorSimList('Da', self.diff_data)
- self.diff_data.theta_sim = DiffTensorSimList('theta', self.diff_data)
- self.diff_data.phi_sim = DiffTensorSimList('phi', self.diff_data)
+ Axx = -16.6278
+ Ayy = 6.13037
+ Axy = 7.65639
+ Axz = -1.89157
+ Ayz = 19.2561
+
+ # Set the MC sim alignment parameter lists.
+ self.align_data.Axx_sim = AlignTensorSimList('Axx', self.align_data)
+ self.align_data.Ayy_sim = AlignTensorSimList('Ayy', self.align_data)
+ self.align_data.Axy_sim = AlignTensorSimList('Axy', self.align_data)
+ self.align_data.Axz_sim = AlignTensorSimList('Axz', self.align_data)
+ self.align_data.Ayz_sim = AlignTensorSimList('Ayz', self.align_data)
# Append the values.
- self.diff_data.tm_sim.append(tm)
- self.diff_data.Da_sim.append(Da)
- self.diff_data.theta_sim.append(theta)
- self.diff_data.phi_sim.append(phi)
-
- # Test the set values.
- self.assertEqual(self.diff_data.type, 'spheroid')
- self.assertEqual(self.diff_data.tm_sim[0], tm)
- self.assertEqual(self.diff_data.Da_sim[0], Da)
- self.assertEqual(self.diff_data.theta_sim[0], theta)
- self.assertEqual(self.diff_data.phi_sim[0], phi)
-
- # Calculate the diffusion tensor objects.
- Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor =
self.calc_spheroid_objects(tm, Da, theta, phi)
-
- # Test the automatically created values.
- self.assertEqual(self.diff_data.Diso_sim[0], Diso)
- self.assertEqual(self.diff_data.Dpar_sim[0], Dpar)
- self.assertEqual(self.diff_data.Dper_sim[0], Dper)
- self.assertEqual(self.diff_data.Dratio_sim[0], Dratio)
-
- # Test the vectors.
- self.assertEqual(self.diff_data.Dpar_unit_sim[0].tostring(),
Dpar_unit.tostring())
-
- # Test the matrices.
- self.assertEqual(self.diff_data.tensor_diag_sim[0].tostring(),
tensor_diag.tostring())
- self.assertEqual(self.diff_data.rotation_sim[0].tostring(),
rotation.tostring())
- self.assertEqual(self.diff_data.tensor_sim[0].tostring(),
tensor.tostring())
-
-
- def test_set_Diso(self):
- """Test that the Diso parameter cannot be set."""
-
- # Assert that a RelaxError occurs when Diso is set (to the tm value
of 10 ns).
- self.assertRaises(RelaxError, setattr, self.diff_data, 'Diso',
1/(6*1e-8))
-
- # Make sure that the Diso parameter has not been set.
- self.assert_(not hasattr(self.diff_data, 'Diso'))
-
-
- def test_set_spheroid_errors(self):
+ self.align_data.Axx_sim.append(Axx)
+ self.align_data.Ayy_sim.append(Ayy)
+ self.align_data.Axy_sim.append(Axy)
+ self.align_data.Axz_sim.append(Axz)
+ self.align_data.Ayz_sim.append(Ayz)
+
+ # Test the set values.
+ self.assertEqual(self.align_data.Axx_sim[0], Axx)
+ self.assertEqual(self.align_data.Ayy_sim[0], Ayy)
+ self.assertEqual(self.align_data.Axy_sim[0], Axy)
+ self.assertEqual(self.align_data.Axz_sim[0], Axz)
+ self.assertEqual(self.align_data.Ayz_sim[0], Ayz)
+
+ # Calculate the diffusion tensor objects.
+ Azz, Axxyy, tensor_diag = self.calc_objects(Axx, Ayy, Axy, Axz, Ayz)
+
+ # Test the automatically created values.
+ self.assertEqual(self.align_data.Azz_sim[0], Azz)
+ self.assertEqual(self.align_data.Axxyy_sim[0], Axxyy)
+
+ # Test the matrices.
+ self.assertEqual(self.align_data.tensor_diag_sim[0].tostring(),
tensor_diag.tostring())
+
+
+ def test_set_Azz(self):
+ """Test that the Azz parameter cannot be set."""
+
+ # Assert that a RelaxError occurs when Azz is set.
+ self.assertRaises(RelaxError, setattr, self.align_data, 'Azz', -23.0)
+
+ # Make sure that the Azz parameter has not been set.
+ self.assert_(not hasattr(self.align_data, 'Azz'))
+
+
+ def test_set_errors(self):
"""Test the setting of spheroidal diffusion tensor parameter errors.
The following parameter errors will be set:
- tm: 1 ns
- Da: 1e3
- theta: 3 degrees
- phi: 5 degrees
+ Axx: 0.3 Hz
+ Ayy: 0.5 Hz
+ Axy: 0.4 Hz
+ Axz: 0.1 Hz
+ Ayz: 0.2 Hz
"""
# The parameter errors.
- tm = 1e-8
- Da = 1e3
- theta = (3 / 360.0) * 2.0 * pi
- phi = (5 / 360.0) * 2.0 * pi
-
- # Set the diffusion type.
- self.diff_data.type = 'spheroid'
+ Axx = 0.3
+ Ayy = 0.5
+ Axy = 0.4
+ Axz = 0.1
+ Ayz = 0.2
# Set the diffusion parameters.
- self.diff_data.tm_err = tm
- self.diff_data.Da_err = Da
- self.diff_data.theta_err = theta
- self.diff_data.phi_err = phi
-
- # Test the set values.
- self.assertEqual(self.diff_data.type, 'spheroid')
- self.assertEqual(self.diff_data.tm_err, tm)
- self.assertEqual(self.diff_data.Da_err, Da)
- self.assertEqual(self.diff_data.theta_err, theta)
- self.assertEqual(self.diff_data.phi_err, phi)
-
- # Calculate the diffusion tensor objects.
- Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor =
self.calc_spheroid_objects(tm, Da, theta, phi)
-
- # Test the automatically created values.
- self.assertEqual(self.diff_data.Diso_err, Diso)
- self.assertEqual(self.diff_data.Dpar_err, Dpar)
- self.assertEqual(self.diff_data.Dper_err, Dper)
- self.assertEqual(self.diff_data.Dratio_err, Dratio)
-
- # Test the vectors.
- self.assertEqual(self.diff_data.Dpar_unit_err.tostring(),
Dpar_unit.tostring())
-
-
- def test_set_spheroid_params(self):
- """Test the setting of spheroidal diffusion tensor parameters.
+ self.align_data.Axx_err = Axx
+ self.align_data.Ayy_err = Ayy
+ self.align_data.Axy_err = Axy
+ self.align_data.Axz_err = Axz
+ self.align_data.Ayz_err = Ayz
+
+ # Test the set values.
+ self.assertEqual(self.align_data.Axx_err, Axx)
+ self.assertEqual(self.align_data.Ayy_err, Ayy)
+ self.assertEqual(self.align_data.Axy_err, Axy)
+ self.assertEqual(self.align_data.Axz_err, Axz)
+ self.assertEqual(self.align_data.Ayz_err, Ayz)
+
+ # Calculate the diffusion tensor objects.
+ Azz, Axxyy, tensor_diag = self.calc_objects(Axx, Ayy, Axy, Axz, Ayz)
+
+ # Test the automatically created values.
+ self.assertEqual(self.align_data.Azz_err, Azz)
+ self.assertEqual(self.align_data.Axxyy_err, Axxyy)
+
+ # Test the matrices.
+ self.assertEqual(self.align_data.tensor_diag_err.tostring(),
tensor_diag.tostring())
+
+
+ def test_set_params(self):
+ """Test the setting of alignment tensor parameters.
The following parameters will be set:
- tm: 20 ns
- Da: 2e6
- theta: 60 degrees
- phi: 290 degrees
+ Axx: -16.6278 Hz
+ Ayy: 6.13037 Hz
+ Axy: 7.65639 Hz
+ Axz: -1.89157 Hz
+ Ayz: 19.2561 Hz
"""
# The parameter values.
- tm = 2e-8
- Da = 2e6
- theta = (60 / 360.0) * 2.0 * pi
- phi = (290 / 360.0) * 2.0 * pi
-
- # Set the diffusion type.
- self.diff_data.type = 'spheroid'
+ Axx = -16.6278
+ Ayy = 6.13037
+ Axy = 7.65639
+ Axz = -1.89157
+ Ayz = 19.2561
# Set the diffusion parameters.
- self.diff_data.tm = tm
- self.diff_data.Da = Da
- self.diff_data.theta = theta
- self.diff_data.phi = phi
-
- # Test the set values.
- self.assertEqual(self.diff_data.type, 'spheroid')
- self.assertEqual(self.diff_data.tm, tm)
- self.assertEqual(self.diff_data.Da, Da)
- self.assertEqual(self.diff_data.theta, theta)
- self.assertEqual(self.diff_data.phi, phi)
-
- # Calculate the diffusion tensor objects.
- Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor =
self.calc_spheroid_objects(tm, Da, theta, phi)
-
- # Test the automatically created values.
- self.assertEqual(self.diff_data.Diso, Diso)
- self.assertEqual(self.diff_data.Dpar, Dpar)
- self.assertEqual(self.diff_data.Dper, Dper)
- self.assertEqual(self.diff_data.Dratio, Dratio)
-
- # Test the vectors.
- self.assertEqual(self.diff_data.Dpar_unit.tostring(),
Dpar_unit.tostring())
-
- # Test the matrices.
- self.assertEqual(self.diff_data.tensor_diag.tostring(),
tensor_diag.tostring())
- self.assertEqual(self.diff_data.rotation.tostring(),
rotation.tostring())
- self.assertEqual(self.diff_data.tensor.tostring(), tensor.tostring())
-
-
- def test_set_spheroid_sim(self):
- """Test the setting of Monte Carlo simulation spheroidal diffusion
tensor parameters.
+ self.align_data.Axx = Axx
+ self.align_data.Ayy = Ayy
+ self.align_data.Axy = Axy
+ self.align_data.Axz = Axz
+ self.align_data.Ayz = Ayz
+
+ # Test the set values.
+ self.assertEqual(self.align_data.Axx, Axx)
+ self.assertEqual(self.align_data.Ayy, Ayy)
+ self.assertEqual(self.align_data.Axy, Axy)
+ self.assertEqual(self.align_data.Axz, Axz)
+ self.assertEqual(self.align_data.Ayz, Ayz)
+
+ # Calculate the diffusion tensor objects.
+ Azz, Axxyy, tensor_diag = self.calc_objects(Axx, Ayy, Axy, Axz, Ayz)
+
+ # Test the automatically created values.
+ self.assertEqual(self.align_data.Azz, Azz)
+ self.assertEqual(self.align_data.Axxyy, Axxyy)
+
+ # Test the matrices.
+ self.assertEqual(self.align_data.tensor_diag.tostring(),
tensor_diag.tostring())
+
+
+ def test_set_sim(self):
+ """Test the setting of Monte Carlo simulation alignment tensor
parameters.
Firstly the following parameters will be appended to empty lists:
- tm: 2 ns
- Da: 1e5
- theta: 0 degrees
- phi: 360 degrees
+ Axx: -16.6278 Hz
+ Ayy: 6.13037 Hz
+ Axy: 7.65639 Hz
+ Axz: -1.89157 Hz
+ Ayz: 19.2561 Hz
These MC sim values will then be explicity overwritten by setting
the first elements of the
lists to:
- tm: 0.5 ns
- Da: 3e5
- theta: 2 degrees
- phi: 0 degrees
- """
-
- # Set the diffusion type.
- self.diff_data.type = 'spheroid'
-
- # Set the MC sim diffusion parameter lists.
- self.diff_data.tm_sim = DiffTensorSimList('tm', self.diff_data)
- self.diff_data.Da_sim = DiffTensorSimList('Da', self.diff_data)
- self.diff_data.theta_sim = DiffTensorSimList('theta', self.diff_data)
- self.diff_data.phi_sim = DiffTensorSimList('phi', self.diff_data)
+ Axx: 0.3 Hz
+ Ayy: 0.5 Hz
+ Axy: 0.4 Hz
+ Axz: 0.1 Hz
+ Ayz: 0.2 Hz
+ """
+
+ # Set the MC sim alignment parameter lists.
+ self.align_data.Axx_sim = AlignTensorSimList('Axx', self.align_data)
+ self.align_data.Ayy_sim = AlignTensorSimList('Ayy', self.align_data)
+ self.align_data.Axy_sim = AlignTensorSimList('Axy', self.align_data)
+ self.align_data.Axz_sim = AlignTensorSimList('Axz', self.align_data)
+ self.align_data.Ayz_sim = AlignTensorSimList('Ayz', self.align_data)
# Append the initial values.
- self.diff_data.tm_sim.append(2e-9)
- self.diff_data.Da_sim.append(1e5)
- self.diff_data.theta_sim.append(0.0)
- self.diff_data.phi_sim.append(2.0 * pi)
+ self.align_data.Axx_sim.append(-16.6278)
+ self.align_data.Ayy_sim.append(6.13037)
+ self.align_data.Axy_sim.append(7.65639)
+ self.align_data.Axz_sim.append(-1.89157)
+ self.align_data.Ayz_sim.append(19.2561)
# The new MC sim parameter values.
- tm = 0.5e-9
- Da = 3e5
- theta = (2 / 360.0) * 2.0 * pi
- phi = 0.0
+ Axx = 0.3
+ Ayy = 0.5
+ Axy = 0.4
+ Axz = 0.1
+ Ayz = 0.2
# Set the MC sim parameter values (overwriting the initial values).
- self.diff_data.tm_sim[0] = tm
- self.diff_data.Da_sim[0] = Da
- self.diff_data.theta_sim[0] = theta
- self.diff_data.phi_sim[0] = phi
-
- # Test the set values.
- self.assertEqual(self.diff_data.type, 'spheroid')
- self.assertEqual(self.diff_data.tm_sim[0], tm)
- self.assertEqual(self.diff_data.Da_sim[0], Da)
- self.assertEqual(self.diff_data.theta_sim[0], theta)
- self.assertEqual(self.diff_data.phi_sim[0], phi)
-
- # Calculate the diffusion tensor objects.
- Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor =
self.calc_spheroid_objects(tm, Da, theta, phi)
-
- # Test the automatically created values.
- self.assertEqual(self.diff_data.Diso_sim[0], Diso)
- self.assertEqual(self.diff_data.Dpar_sim[0], Dpar)
- self.assertEqual(self.diff_data.Dper_sim[0], Dper)
- self.assertEqual(self.diff_data.Dratio_sim[0], Dratio)
-
- # Test the vectors.
- self.assertEqual(self.diff_data.Dpar_unit_sim[0].tostring(),
Dpar_unit.tostring())
-
- # Test the matrices.
- self.assertEqual(self.diff_data.tensor_diag_sim[0].tostring(),
tensor_diag.tostring())
- self.assertEqual(self.diff_data.rotation_sim[0].tostring(),
rotation.tostring())
- self.assertEqual(self.diff_data.tensor_sim[0].tostring(),
tensor.tostring())
-
-
- def test_set_tm(self):
- """Test the setting of the tm parameter.
-
- The tm parameter will be set to 10 ns. The setting of tm should
automatically create the
- Diso parameter.
- """
-
- # Set the diffusion type.
- self.diff_data.type = 'sphere'
-
- # Set the tm value to 10 ns.
- self.diff_data.tm = 1e-8
-
- # Test that the tm parameter has been set correctly.
- self.assert_(hasattr(self.diff_data, 'tm'))
- self.assertEqual(self.diff_data.tm, 1e-8)
-
- # Test that the Diso parameter has been set correctly.
- self.assert_(hasattr(self.diff_data, 'Diso'))
- self.assertEqual(self.diff_data.Diso, 1/(6*1e-8))
+ self.align_data.Axx_sim[0] = Axx
+
+ # Test the set values.
+ self.assertEqual(self.align_data.Axx_sim[0], Axx)
+ self.assertEqual(self.align_data.Ayy_sim[0], Ayy)
+ self.assertEqual(self.align_data.Axy_sim[0], Axy)
+ self.assertEqual(self.align_data.Axz_sim[0], Axz)
+ self.assertEqual(self.align_data.Ayz_sim[0], Ayz)
+
+ # Calculate the diffusion tensor objects.
+ Azz, Axxyy, tensor_diag = self.calc_objects(Axx, Ayy, Axy, Axz, Ayz)
+
+ # Test the automatically created values.
+ self.assertEqual(self.align_data.Azz_sim[0], Azz)
+ self.assertEqual(self.align_data.Axxyy_sim[0], Axxyy)
+
+ # Test the matrices.
+ self.assertEqual(self.align_data.tensor_diag_sim[0].tostring(),
tensor_diag.tostring())
+
+
+ def test_set_Axx(self):
+ """Test the setting of the Axx parameter."""
+
+ # Set the Axx value to 10 Hz.
+ self.align_data.Axx = 10.0
+
+ # Test that the Axx parameter has been set correctly.
+ self.assert_(hasattr(self.align_data, 'Axx'))
+ self.assertEqual(self.align_data.Axx, 10.0)
r4055 - /branches/N_state_model/test_suite/unit_tests/_data/test_align_tensor.py